3GHN | pdb_00003ghn

Crystal structure of the exosite-containing fragment of human ADAMTS13 (form-2)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.280 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.229 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.229 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

This is version 2.2 of the entry. See complete history. 


Literature

Crystal structures of the non-catalytic domains of ADAMTS13 reveal multiple discontinuous exosites for von Willebrand factor

Akiyama, M., Takeda, S., Kokame, K., Takagi, J., Miyata, T.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A disintegrin and metalloproteinase with thrombospondin motifs 13419Homo sapiensMutation(s): 1 
Gene Names: ADAMTS13
EC: 3.4.24 (PDB Primary Data), 3.4.24.87 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q76LX8 (Homo sapiens)
Explore Q76LX8 
Go to UniProtKB:  Q76LX8
PHAROS:  Q76LX8
GTEx:  ENSG00000160323 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ76LX8
Glycosylation
Glycosylation Sites: 4
Go to GlyGen: Q76LX8-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-glucopyranose-(1-3)-alpha-L-fucopyranose
C
2O-Glycosylation
Glycosylation Resources
GlyTouCan:  G36855WW
GlyCosmos:  G36855WW
GlyGen:  G36855WW
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.280 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.229 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.229 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.577α = 90
b = 51.37β = 106.75
c = 76.371γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
SOLVEphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2021-11-10
    Changes: Database references, Structure summary
  • Version 2.2: 2024-11-20
    Changes: Data collection, Structure summary